[gmx-users] Seg Fault with Gromacs gmx grompp command - Intel compiler

Mark Abraham mark.j.abraham at gmail.com
Fri Dec 6 15:39:19 CET 2019 

OK, that looks fine.

What does the stack trace of the segfault look like? e.g.

gdb --args /the/gmx grompp -whatever -args

Mark

On Fri, 6 Dec 2019 at 15:29, Glenn (Gedaliah) Wolosh <gwolosh at njit.edu>
wrote:

>
>
> > On Dec 6, 2019, at 9:12 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> >
> > Hi,
> >
> > If the environment is sufficiently well constructed to do the necessary
> > dynamic linking, then things like gmx -version and gmx editconf should
> not
> > segfault. Do they? My guess is that the appropriate Intel libraries, or
> > perhaps the gcc libstdc++ libraries that icc requires are actually not
> > available in the environment.
>
>
> These command do not segfault. The dynamic linking is fine.
>
> kong-183 lysozyme >: module list
> Currently Loaded Modulefiles:
>   1) sge                            3) intel/parallel_studio/2019.4   5)
> gromacs/intel/2019.4
>   2) singularity/3.2.1              4) gcc/5.4.0
>
> kong-184 lysozyme >: which gmx
> /afs/cad/linux/gromacs/intel/2019.4/bin/gmx
> kong-185 lysozyme >: ldd /afs/cad/linux/gromacs/intel/2019.4/bin/gmx
>         linux-vdso.so.1 =>  (0x00007ffd08584000)
>         libmkl_intel_lp64.so =>
> /afs/cad/linux/intel/parallel_studio_cluster_edition_2019.4/compilers_and_libraries_2019.4.243/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so
> (0x00002afa6906e000)
>         libmkl_sequential.so =>
> /afs/cad/linux/intel/parallel_studio_cluster_edition_2019.4/compilers_and_libraries_2019.4.243/linux/mkl/lib/intel64_lin/libmkl_sequential.so
> (0x00002afa69be6000)
>         libmkl_core.so =>
> /afs/cad/linux/intel/parallel_studio_cluster_edition_2019.4/compilers_and_libraries_2019.4.243/linux/mkl/lib/intel64_lin/libmkl_core.so
> (0x00002afa6b180000)
>         libgromacs.so.4 =>
> /afs/cad/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4
> (0x00002afa6f455000)
>         libm.so.6 => /lib64/libm.so.6 (0x00000038cc400000)
>         libstdc++.so.6 =>
> /afs/cad/linux/gcc-5.4.0-sl6/lib64/libstdc++.so.6 (0x00002afa706fe000)
>         libiomp5.so =>
> /afs/cad/linux/intel/parallel_studio_cluster_edition_2019.4/compilers_and_libraries_2019.4.243/linux/compiler/lib/intel64_lin/libiomp5.so
> (0x00002afa70a8c000)
>         libgcc_s.so.1 => /afs/cad/linux/gcc-5.4.0-sl6/lib64/libgcc_s.so.1
> (0x00002afa70e76000)
>         libpthread.so.0 => /lib64/libpthread.so.0 (0x00000038cbc00000)
>         libc.so.6 => /lib64/libc.so.6 (0x00000038cb800000)
>         libdl.so.2 => /lib64/libdl.so.2 (0x00000038cc000000)
>         librt.so.1 => /lib64/librt.so.1 (0x00000038cc800000)
>         libimf.so =>
> /afs/cad/linux/intel/parallel_studio_cluster_edition_2019.4/compilers_and_libraries_2019.4.243/linux/compiler/lib/intel64_lin/libimf.so
> (0x00002afa7108e000)
>         libsvml.so =>
> /afs/cad/linux/intel/parallel_studio_cluster_edition_2019.4/compilers_and_libraries_2019.4.243/linux/compiler/lib/intel64_lin/libsvml.so
> (0x00002afa7162f000)
>         libirng.so =>
> /afs/cad/linux/intel/parallel_studio_cluster_edition_2019.4/compilers_and_libraries_2019.4.243/linux/compiler/lib/intel64_lin/libirng.so
> (0x00002afa72fd3000)
>         libintlc.so.5 =>
> /afs/cad/linux/intel/parallel_studio_cluster_edition_2019.4/compilers_and_libraries_2019.4.243/linux/compiler/lib/intel64_lin/libintlc.so.5
> (0x00002afa73345000)
>         /lib64/ld-linux-x86-64.so.2 (0x00005613d5ea5000)
>
> This seems specific to the Scientific Linux 6.x OS.  When built and
> installed on a 7.x version, cmx grompp works fine.
>
> GW
>
>
>
> >
> > Mark
> >
> > On Thu, 5 Dec 2019 at 21:36, Glenn (Gedaliah) Wolosh <gwolosh at njit.edu
> <mailto:gwolosh at njit.edu>>
> > wrote:
> >
> >> Thanks for the quick response. I do have the environment properly
> prepare
> >> via modules.
> >>
> >> GW
> >>
> >>
> >>> On Dec 5, 2019, at 3:24 PM, Mark Abraham <mark.j.abraham at gmail.com>
> >> wrote:
> >>>
> >>> Hi,
> >>>
> >>> I suspect you need to prepare the intel environment at run time like
> you
> >>> did before compilation. Probably you (or a module you loaded) source-d
> a
> >>> compilervars.sh file, and that's probably what you need here.
> >>>
> >>> Mark
> >>>
> >>> On Thu, 5 Dec 2019 at 20:22, Glenn (Gedaliah) Wolosh <gwolosh at njit.edu
> >> <mailto:gwolosh at njit.edu <mailto:gwolosh at njit.edu>>>
> >>> wrote:
> >>>
> >>>>
> >>>> Also posted on the intel forum:
> >>>>
> >>>> This problem is consistent with the following gromacs/compiler
> versions:
> >>>>
> >>>> Gromacs 2019.4/Intel Parallel Studio 2019.4
> >>>>
> >>>> Gromacs 2019.4/Intel 2017.2
> >>>>
> >>>> Gromacs 2018.2/Intel Parallel Studio 2019.4
> >>>>
> >>>> Gromacs 2018.5/Intel Parallel Studio 2019.4
> >>>>
> >>>> The command to build and install gromacs in all cases is
> >>>>
> >>>> export CC=icc
> >>>> export CXX=icpc
> >>>> export FC=ifort
> >>>>
> >>>> cmake ..  -DGMX_FFT_LIBRARY=mkl \
> >>>>
>  -DCMAKE_INSTALL_PREFIX=$HOME/sw/gromacs/intel/<version>
> >>>> &&  make VERBOSE=1 && make install
> >>>>
> >>>> The gcc version in the PATH is 5.4.0
> >>>>
> >>>> The OS is:
> >>>>
> >>>> Scientific Linux release 6.10 (Carbon)
> >>>>
> >>>> I am running the lysozyme tutorial:
> >>>> http://www.mdtutorials.com/gmx/lysozyme/ <
> >>>> http://www.mdtutorials.com/gmx/lysozyme/ <
> >> http://www.mdtutorials.com/gmx/lysozyme/ <
> http://www.mdtutorials.com/gmx/lysozyme/>>>
> >>>> The command that seg faults is
> >>>>
> >>>> gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
> >> -maxwarn 2
> >>>>
> >>>> The gmx grompp command succeeds when using a version of gromacs
> compiled
> >>>> with GCC
> >>>>
> >>>> Any help would be greatly appreciated.
> >>>>
> >>>>
> >>>> GW
> >>>> --
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> >>>>
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